Endogenous geminivirus-like elements in the genus Rhododendron provide insights into the evolutionary origins of the begomovirus nuclear shuttle protein.

Geminiviruses constitute a diverse group of plant viruses with small, circular single-stranded DNA genomes. While most geminiviruses possess monopartite genomes, the genus Begomovirus uniquely includes both monopartite and bipartite members. The evolutionary origin of the second component of begomovirus (DNA-B) has been a subject of considerable debate. Two primary hypotheses propose that DNA-B originated from a modified monopartite genome or through the capture of a satellite DNA. Recent discoveries of unclassified bipartite geminiviruses call for a reevaluation of these hypotheses. To address this, we investigated the evolutionary history of the begomovirus nuclear shuttle protein (NSP) through homolog searches, comparative genomics, and structural protein analyses. Our findings unambiguously demonstrated that NSP is homologous to the coat protein (CP) but originated from a CP encoded by an ancient geminivirus lineage, distinct from begomoviruses. This ancient lineage is represented by bipartite viruses integrated into plant genomes of the genus Rhododendron. These results challenge the prevailing paradigm regarding the evolutionary origin of NSP and offer new insights into the evolution of begomovirus genome architecture.